Browsing by Subject "SNPs"
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Item Ancestry Informative Markers Tailored to Hispanic Populations(2020-05) Setser, Casandra H.; Cross, Deanna S.; Planz, John V.; Barber, Robert C.; Phillips, Nicole R.; Krishnamoorthy, Raghu R.Hispanic populations are highly heterogeneous despite being grouped together as a conglomerate population; this makes an accurate panel of ancestry informative markers (AIMs) especially important for human identification. In Chapter 2, the Genomic Origins and Admixture in Latinos (GOAL) dataset containing 494,886 SNPs was used for SNP ascertainment. Utilizing a country attributable variant of Wright's FST, 234 SNPs were selected for biogeographic ancestry (BGA) determination by tailoring each SNP to genetic differentiation of specific populations. Accuracy of BGA prediction was tested using multinomial logistic regression (MLR) and as few as 55 SNPs were robust to 90% for all populations studied. The panel of 234 SNPs was compressed by 65.8% to 80 SNPs by decreasing the influence of Honduras and the Dominican Republic SNPs with high country attributable mean FST values in favor of additional SNPs for Colombia, Cuba, and Puerto Rico; this balanced small panel size with classification accuracy. In Chapter 3, the Setser80 Hispanic AIMs panel was tested against the panels of 128 SNPs developed by the Seldin group and 55 SNPs developed by the Kidd group using STRUCTURE, PCA, a naive Bayesian classifier and MLR. In STRUCTURE, the Setser80 was able to distinguish Honduras, the Dominican Republic, and Colombia at K=4, where the Seldin and Kidd panels were optimized at K=3 and distinguished only Honduras and the Dominican Republic; similar results were obtained by PCA. The GOAL dataset was combined with the Admixed American super-population from the 1000 Genomes Project to test the panel on an expanded dataset of seven populations. Overall, the Setser80 had superior results to the Seldin and Kidd panels with 91.5% accuracy by naive Bayesian classifier and 93.2% by MLR. As an indication of its portability, the Setser80 had accuracies of >98% for Peru and >80% for Mexicans living in Los Angeles, which were not involved in SNP ascertainment. Given its accuracy and lack of overlap, the Setser80 may supplement existing panels for more granular Hispanic BGA determination. In Chapter 4, the application of allele frequencies to forensic genetics, genealogy, and clinical genetics are discussed as well as future directions and ethical considerations.Item skater: an R package for SNP-based kinship analysis, testing, and evaluation(F1000 Research Ltd., 2022-01-07) Turner, Stephen D.; Nagraj, V. P.; Scholz, Matthew; Jessa, Shakeel; Acevedo, Carlos; Ge, Jianye; Woerner, August E.; Budowle, BruceMotivation: SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream process- ing and manipulation. A dedicated software package that consistently and intuitively imple- ments this analysis functionality is needed. Results: Here we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R. The skater package contains a suite of well-documented tools for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing IBD segment data. Availability: The skater package is implemented as an R package and is released under the MIT license at https://github.com/signaturescience/skater. Documentation is available at https://signaturescience.github.io/skater.Item Typing Highly Degraded DNA Using Target Enrichment(2020-05) Kieser, Rachel E.; Budowle, Bruce; Phillips, Nicole R.; Coble, Michael D.; Berg, Rance E.; Salvatore, MichaelForensic genetic profiling is the process of targeting unique positions within the human genome for identity testing of biological DNA evidence. Forensic profiling of highly degraded DNA samples is one of the primary challenges faced by forensic analysts. These compromised biological samples are difficult to genetically profile, due to the highly fragmented nature of the target molecules, using traditional methods which centers around the detection of short tandem repeats (STRs). For STR typing to be successful, DNA must be relatively intact in order to amplify by PCR. Molecular biology approaches have been developed that may be applied to severely degraded samples to increase the capability of DNA profiling. Targeting single nucleotide polymorphisms (SNPs) holds potential as their amplicons can be designed to be substantially smaller than those for STRs, making these markers a viable alternative for typing degraded (fragmented) DNA. Additionally, rolling circle amplification (RCA) can be exploited as a tool as it has the capacity to amplify all genomic DNA in a circular template present in a sample. A circular molecule essentially creates an infinitely long template for amplification. RCA generates linear tandem copies of the circular template sequence. However, nuclear DNA is not circular and thus RCA cannot be used to its full potential. CircLigase II is an enzyme that circularizes single-stranded DNA. Thus, it may be possible to generate circular DNA from the highly degraded fragments of challenged samples. Molecular inversion probes (MIPs) are an alternative circle-based enrichment approach. A MIP is a single-stranded oligonucleotide that contains two target-specific arms flanking a SNP of interest (capture) and internal PCR primer binding sites for controlled amplification. The two target-specific arms hybridize to the target DNA, the gap is filled resulting in the complementary state of the SNP of interest, the MIP dissociates from the target, and the target site is amplified employing the internally incorporated primer binding sites. Coupled to massively parallel sequencing (MPS), both circle-based approaches were attempted with limited to no success. Reverse Complement PCR (RC-PCR) was pursued to address the same problem of analyzing degraded DNA. RC-PCR is an innovative, one-step PCR target enrichment technology adapted for the amplification of highly degraded (fragmented) DNA. It provides simultaneous amplification and tagging of a targeted sequence construct in a single, closed-tube assay. A human identification (HID) RC-PCR panel was designed targeting 27 identity SNPs generating targets only 50 base pairs in length. In a single reaction, the complete sequencing construct is produced which is essential for MPS library preparation. The RC-PCR approach produced reliable and concordant genotyping results as well as demonstrated a sensitivity of detection of a majority of alleles down to 60 pg of input DNA. In addition, RC-PCR showed robustness tolerating known PCR inhibitors, especially calcium and collagen. The RC-PCR system may be an effective alternative to current forensic genetic methods in the analysis of highly degraded DNA.Item Validation of Four Multiplex SNP Panels for Forensic DNA Testing: An Assessment of the Sensitivity and Reproducibility of the SNaPshot Primer Extension Assay(2003-05-01) Dutton, Kristi R.; John Planz; Arthur Eisenberg; Joseph WarrenOrchid Cellmark provided four proprietary multiplex SNP primer panels, each of which has been developed to identify 10-12 SNPs using a modified version of the SNaPshot Mutliplex protocol. The commercially available STR typing kits routinely used in forensic testing require an input of between 0.5 to 2ng of DNA. Orchid Cellmark has suggested using 2ng of DNA with each of their multiplex SNP primer panels. However, preliminary data has indicated that as little as 100pg of DNA can yield results with many of the SNP markers. Several methods of SNP detection exist. This project relied on the use of multiplex SNP extension primers in conjunction with the ABI SNaPshot Multiplex Kit (Applied Biosystems, Foster City, CA) to identify SNPs in the nuclear genome. Analysis of 50 or more SNPs would be very laborious if single-tube polymerase chain reaction (PCR) was used for sample testing. Multiplexing SNP primers to include 10-12 per reaction tube will increase the throughput of SNP analysis. The cost of analysis can also be reduced using multiplexes since the amount of reagents per SNP is decreased. This project determined if the SNaPshot extension assay used in conjunction with the Orchid Cellmark multiplex panels could accurately detect SNPs at quantities less than 2ng DNA on a capillary electrophoresis (CE) platform.